3590 Stephenson Life Sciences Research Center
101 Stephenson Parkway
Norman, OK 73019
Alternate office: 28 George Lynn Cross Hall
Education:
B.S., University of Rochester, 1995
PhD., University of Rochester, 2002
Postdoc, Yale University, 2002-2005
Research areas:
Molecular and Cellular Biology, Structural Biology, Biophysics, RNA Biology, Biochemistry, Biophysical Chemistry, Virology, Bioinformatics
Research interests:
The power of RNA to regulate gene expression energizes the Schroeder lab. RNA, ribonucleic acid, folds into three-dimensional structures and thus achieves specificity in molecular recognition and enzymatic activity. Toward the long-term goal of RNA structure prediction from sequence, the Schroeder lab explores the structures of encapsidated satellite tobacco mosaic virus (STMV) RNA, the structures and energetics of prohead RNA (pRNA), and the thermodynamic stabilities of noncanonical pairs at RNA helix ends. None of these RNA structures are currently predicted well. Thus discovering new properties of these RNA structures and energetics will provide new insight into the fundamental physical forces that direct RNA folding and function. Additional experimental data about RNA conformations, such as chemical modification, phylogenetic covariation, improved thermodynamic parameters, and the magnesium dependence of RNA tertiary interactions, can further define the RNA conformational landscape and improve RNA structure predictions. Information from a variety of experiments including UV optical melting, NMR, crystallography, chemical probing, as well as standard molecular biology and biochemistry techniques, will be required to solve these problems. New computational tools are necessary to incorporate this new data into structure predictions. The lessons learned from solving these challenging problems will contribute to understanding the fundamental interactions that determine RNA structure and function and thus lead to better RNA structure predictions. Accurate RNA structure predictions can direct studies of RNA function and rational design of therapeutics that target viral RNA. Viruses, such as flu, HIV-1, hepatitis, and the common cold, have RNA genomes, and few remedies are available to treat these diseases. Many antibiotics target ribosomal RNA, and viral RNAs provide a gold mine of undeveloped therapeutic target sites
Relevant publications:
“Perspectives on Viral RNA Genomes and the RNA Folding Problem.” S.J. Schroeder. Viruses 12, 1126 (2020).
“Challenges and Approaches to Predicting RNA with Multiple Functional Structures.” S.J. Schroeder. RNA 24, 1615-1624 (2018).
“Advancing Viral RNA Structure Prediction: Measuring the Thermodynamics of Pyrimidine-Rich Internal Loops.” A. Phan, K. Mailey, J. Saeki, X. Gu, Schroeder, S.J. RNA. 23, 770-781 (2017).
“Thermodynamic Stabilities of Three-way Junction Nanomotifs in Prohead RNA.” A.C. Hill, S.J. Schroeder, RNA 23, 521-529 (2017).
“NMR Structures and Dynamics in a Prohead RNA Loop that Binds Metal Ions.” X. Gu , S.-Y. Park, M. Tonnelli, G. Cornilescu, T. Xia, D. Zhong, S.J. Schroeder, J. Phys. Chem. Lett. 7, 3841-3846(2016).
Gu, X., Nguyen, MT, Overacre, A., Seaton, S., Schroeder, SJ. Effects of salt, polyethylene glycol, and locked nucleic acids on the thermodynamic stabilities of consecutive terminal adenosine mismatches in RNA duplexes. J. Phys. Chem. B., 2013; 117: 3531-3540. PMID: 23480443.
Schroeder, SJ, Stone, JW, Bleckley, S, Gibbons, TR, Mathews, D. Ensemble of Secondary Structures for Encapsidated Satellite Tobacco Mosaic Virus RNA Consistent with Constraints from Chemical Probing and Crystallography. Biophys. J. 2011; 101: 167-175. PMID: 21723827.
Gu, X, Schroeder, SJ. Different Sequences Show Similar Quaternary Interaction Stabilities in Prohead Viral RNA Self-Assembly. J. Biol. Chem. 2011; 286: 14419-14426. PMID: 21349846.
Harris, S, Schroeder, SJ. NMR Structure of Prohead RNA E-loop Hairpin. Biochemistry. 2010; 49: 5989-5997. PMID: 20550192.
